Revisiting K-mer Profile for Effective and Scalable Genome Representation Learning
Fuente:
arXiv
Saved in:
| Main Authors: | Celikkanat, Abdulkadir, Masegosa, Andres R., Nielsen, Thomas D. |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
UncertainGen: Uncertainty-Aware Representations of DNA Sequences for Metagenomic Binning
by: Celikkanat, Abdulkadir, et al.
Published: (2025)
by: Celikkanat, Abdulkadir, et al.
Published: (2025)
ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data
by: Jiao, Yifeng, et al.
Published: (2025)
by: Jiao, Yifeng, et al.
Published: (2025)
RNA-GPT: Multimodal Generative System for RNA Sequence Understanding
by: Xiao, Yijia, et al.
Published: (2024)
by: Xiao, Yijia, et al.
Published: (2024)
GraphPINE: Graph Importance Propagation for Interpretable Drug Response Prediction
by: Inoue, Yoshitaka, et al.
Published: (2025)
by: Inoue, Yoshitaka, et al.
Published: (2025)
DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome
by: Zhou, Zhihan, et al.
Published: (2023)
by: Zhou, Zhihan, et al.
Published: (2023)
Unlocking Noisy Real-World Corpora for Foundation Model Pre-Training via Quality-Aware Tokenization
by: Gollwitzer, Arvid E., et al.
Published: (2026)
by: Gollwitzer, Arvid E., et al.
Published: (2026)
Beyond the Alphabet: Deep Signal Embedding for Enhanced DNA Clustering
by: Abraham, Hadas, et al.
Published: (2024)
by: Abraham, Hadas, et al.
Published: (2024)
Dy-mer: An Explainable DNA Sequence Representation Scheme using Dictionary Learning
by: Peng, Zhiyuan, et al.
Published: (2024)
by: Peng, Zhiyuan, et al.
Published: (2024)
SHAP zero Explains Biological Sequence Models with Near-zero Marginal Cost for Future Queries
by: Tsui, Darin, et al.
Published: (2024)
by: Tsui, Darin, et al.
Published: (2024)
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
by: Kim, Jeremie S., et al.
Published: (2019)
by: Kim, Jeremie S., et al.
Published: (2019)
AntigenLM: Structure-Aware DNA Language Modeling for Influenza
by: Pei, Yue, et al.
Published: (2026)
by: Pei, Yue, et al.
Published: (2026)
dnaGrinder: a lightweight and high-capacity genomic foundation model
by: Zhao, Qihang, et al.
Published: (2024)
by: Zhao, Qihang, et al.
Published: (2024)
DNABERT-S: Pioneering Species Differentiation with Species-Aware DNA Embeddings
by: Zhou, Zhihan, et al.
Published: (2024)
by: Zhou, Zhihan, et al.
Published: (2024)
Efficient and Scalable Fine-Tune of Language Models for Genome Understanding
by: Zhan, Huixin, et al.
Published: (2024)
by: Zhan, Huixin, et al.
Published: (2024)
How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences
by: Ouaari, Sofiane, et al.
Published: (2026)
by: Ouaari, Sofiane, et al.
Published: (2026)
scVGAE: A Novel Approach using ZINB-Based Variational Graph Autoencoder for Single-Cell RNA-Seq Imputation
by: Inoue, Yoshitaka
Published: (2024)
by: Inoue, Yoshitaka
Published: (2024)
Gene and RNA Editing: Methods, Enabling Technologies, Applications, and Future Directions
by: Aledhari, Mohammed, et al.
Published: (2024)
by: Aledhari, Mohammed, et al.
Published: (2024)
From In Silico to In Vitro: A Comprehensive Guide to Validating Bioinformatics Findings
by: Wang, Tianyang, et al.
Published: (2025)
by: Wang, Tianyang, et al.
Published: (2025)
TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling
by: Yang, Qirong, et al.
Published: (2025)
by: Yang, Qirong, et al.
Published: (2025)
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data
by: Gong, Jing, et al.
Published: (2023)
by: Gong, Jing, et al.
Published: (2023)
CauSTream: Causal Spatio-Temporal Representation Learning for Streamflow Forecasting
by: Wan, Shu, et al.
Published: (2025)
by: Wan, Shu, et al.
Published: (2025)
Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
by: Li, Zehui, et al.
Published: (2025)
by: Li, Zehui, et al.
Published: (2025)
Meta-Learning on Augmented Gene Expression Profiles for Enhanced Lung Cancer Detection
by: Moghaddam, Arya Hadizadeh, et al.
Published: (2024)
by: Moghaddam, Arya Hadizadeh, et al.
Published: (2024)
Genomic Next-Token Predictors are In-Context Learners
by: Breslow, Nathan, et al.
Published: (2025)
by: Breslow, Nathan, et al.
Published: (2025)
Multimodal 3D Genome Pre-training
by: Yang, Minghao, et al.
Published: (2025)
by: Yang, Minghao, et al.
Published: (2025)
TEPI: Taxonomy-aware Embedding and Pseudo-Imaging for Scarcely-labeled Zero-shot Genome Classification
by: Aakur, Sathyanarayanan, et al.
Published: (2024)
by: Aakur, Sathyanarayanan, et al.
Published: (2024)
Learning Genomic Structure from $k$-mers
by: Thor, Filip, et al.
Published: (2025)
by: Thor, Filip, et al.
Published: (2025)
Revisiting Ensemble Methods for Stock Trading and Crypto Trading Tasks at ACM ICAIF FinRL Contest 2023-2024
by: Holzer, Nikolaus, et al.
Published: (2025)
by: Holzer, Nikolaus, et al.
Published: (2025)
Machine Learning-Based Genomic Linguistic Analysis (Gene Sequence Feature Learning): A Case Study on Predicting Heavy Metal Response Genes in Rice
by: Yang, Ruiqi, et al.
Published: (2025)
by: Yang, Ruiqi, et al.
Published: (2025)
Bitcoin Price Prediction using Machine Learning and Combinatorial Fusion Analysis
by: Wu, Yuanhong, et al.
Published: (2026)
by: Wu, Yuanhong, et al.
Published: (2026)
Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences
by: Li, Zehui, et al.
Published: (2024)
by: Li, Zehui, et al.
Published: (2024)
Celler:A Genomic Language Model for Long-Tailed Single-Cell Annotation
by: Zhao, Huan, et al.
Published: (2025)
by: Zhao, Huan, et al.
Published: (2025)
Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN
by: Refahi, Mohammad Saleh, et al.
Published: (2025)
by: Refahi, Mohammad Saleh, et al.
Published: (2025)
Enhancing Resilience and Scalability in Travel Booking Systems: A Microservices Approach to Fault Tolerance, Load Balancing, and Service Discovery
by: Barua, Biman, et al.
Published: (2024)
by: Barua, Biman, et al.
Published: (2024)
DeepSeq: High-Throughput Single-Cell RNA Sequencing Data Labeling via Web Search-Augmented Agentic Generative AI Foundation Models
by: Dajani, Saleem A. Al, et al.
Published: (2025)
by: Dajani, Saleem A. Al, et al.
Published: (2025)
Enhanced Gene Selection in Single-Cell Genomics: Pre-Filtering Synergy and Reinforced Optimization
by: Zhang, Weiliang, et al.
Published: (2024)
by: Zhang, Weiliang, et al.
Published: (2024)
MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging
by: Li, Siyuan, et al.
Published: (2025)
by: Li, Siyuan, et al.
Published: (2025)
Revolutionizing Genomics with Reinforcement Learning Techniques
by: Karami, Mohsen, et al.
Published: (2023)
by: Karami, Mohsen, et al.
Published: (2023)
DNABERT-2: Fine-Tuning a Genomic Language Model for Colorectal Gene Enhancer Classification
by: King, Darren, et al.
Published: (2025)
by: King, Darren, et al.
Published: (2025)
Deep Learning Models Meet Financial Data Modalities
by: Khubiev, Kasymkhan, et al.
Published: (2025)
by: Khubiev, Kasymkhan, et al.
Published: (2025)
Similar Items
-
UncertainGen: Uncertainty-Aware Representations of DNA Sequences for Metagenomic Binning
by: Celikkanat, Abdulkadir, et al.
Published: (2025) -
ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data
by: Jiao, Yifeng, et al.
Published: (2025) -
RNA-GPT: Multimodal Generative System for RNA Sequence Understanding
by: Xiao, Yijia, et al.
Published: (2024) -
GraphPINE: Graph Importance Propagation for Interpretable Drug Response Prediction
by: Inoue, Yoshitaka, et al.
Published: (2025) -
DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome
by: Zhou, Zhihan, et al.
Published: (2023)